The pullx file should contain everything that you need. dX,dY,dZ *are*
the components of the distances between the two groups.
I still don't understand your question (perhaps you could give us a
worked example with real data?), but if you just want the COM
distance, then try this:
cat pullx.xvg |awk '{print sqrt($1,$5*$5+$6*$6+$7*$7)}' > my.dist
of vourse, what you need depends on your pull code options, but this
should give you a start. Combine this with VMD and you should be able
to figure out what you need.
Chris.
-- original message --
Hi all
In hindsight I think the question I posted yesterday may have been a
little naive. To rephrase it - If the pullx.xvg files contain X Y Z dX
dY dZ, (because pull_dim = Y Y Y), does the g_wham programme calculate
the centre of mass distances to use in the histogram i.e. Will the first
column in the histo.xvg file be the centre of mass distances (the
modulus of the three vector components)?
Cheers
Gavin
Gavin Melaugh wrote:
Hi All
I have generated a series of configurations for two molecules
approaching along the z axis. I am now going to run umbrella sampling of
these configurations at a fixed distance (XYZ) in order to calculate the
PMF. I understand that the output of the pulling code gives a pullx.xvg
file which serves as the input to g_wham. I notice that this file does
not contain the distances between the COMs of the two molecules. Is
there anyway of generating a file that contains such information
directly form mdrun or do I have to run g_dist for every trajectory
generated. If this is the case can the output from g_dist serve as the
input for g_wham (like pullx.xvg).
Cheers
Gavin
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